If you’re a true chocolate lover—this one’s for you. These Double Chocolate Protein Pastries are part muffin top, part soft-baked cookie, and part bakery-style pastry… all filled with small puddles of melty chocolatey goodness. They’re decadent, yet secretly wholesome and protein-filled—so you can satisfy your chocolate cravings and feel good about it.

These pastries were born after my Blueberry Protein Breakfast Pastries went viral—I wanted to create a chocolatey sister recipe that hit the same sweet spot: bakery-level taste with a healthy dose of nutrition. They’re easy to make and extra delicious when they’re warm from the oven.

This recipe’s a hit!

Yum!! I made these completely dairy free using a coconut milk Greek yogurt and a plant protein pancake mix. They are great either as a little after dinner treat or a morning snack with coffee!! Will definitely make these on repeat! Love how quickly they come together!!

MP
(5 stars) 5 ratings
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And here’s a funny thing—sometimes they bake up puffier like buns, and other times they spread a bit wider and flatter like jumbo cookies or thick pancakes. There’s truly no rhyme or reason (believe me, I’ve tested them plenty of times with the exact same ingredients and bake time!). It’s a mystery… but either way, they turn out delicious every single time.

Step 1: In a medium bowl, whisk together the wet ingredients, then add the dry.
Step 2: Stir everything together until just combined.
Step 3: Fold in the chocolate chips gently. The batter will be thick and dough-like—that’s exactly right.
Step 4: Drop ⅓-cup mounds onto the baking sheet, gently shape into rounds, and top with a few extra chocolate chips, and bake.

Why you’ll be sweet on these pastries

  • Protein meets pleasure: Greek yogurt, mixed with the other ingredients, brings a satisfying, nourishing boost.
  • Double the chocolate: Cocoa powder and chocolate chips make every bite dreamy.
  • Easy, breezy bake: One bowl, about 20 minutes, no mixer required.
  • Anytime treat: Chocolate works all day!

Prefer muffins? Bake ’em in a standard muffin tin using the same directions—start checking for doneness at the 15-minute mark.

To cut down on added sugar, simply use sugar-free chocolate chips and a vanilla Greek yogurt sweetened with stevia or monk fruit. You’ll still get full-on chocolate bliss… I’ve tested this method, and it worked out GREAT. Every bite is moist and perfectly sweet, with a hint of cocoa and a satisfying boost of protein!

More chocolate to bake up

If these chocolate dreams win you over (they will!), try my Flourless Protein Brownies for another any-time-of-the-day chocolate fix, or my Chocolate Oatmeal Bake for a yummy breakfast that doubles as dessert. You’ll also love my Energizing Chocolate Muffins—made with chocolate protein powder and espresso—and my 3-Ingredient Chocolate Cookies… don’t forget about those!!

Try my Chocolate Banana Muffins next!

(5 stars) 5 ratings

Double Chocolate Protein Muffin Tops (Soft-Baked)

Scrumptiously soft and studded with melty chocolate chips, these protein-filled goodies strike the perfect balance between indulgence and nourishment. Enjoy one warm from the oven for a wholesome snack that tastes just like dessert.
Yield: 8 pastries
Prep Time: 10 minutes
Cook Time: 15 minutes
Total Time: 35 minutes
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Ingredients
 

  • 1 cup vanilla Greek yogurt, thick-style; mix any liquid on top back in before measuring
  • 2 large eggs, lightly beaten
  • 1 cup protein pancake mix, Kodiak or your favorite brand
  • 2 tablespoons unsweetened cocoa powder
  • 2 teaspoons baking powder
  • ½ teaspoon kosher salt
  • 1 cup semi-sweet chocolate chips, regular or mini
  • ½ teaspoon vanilla extract, if your yogurt is plain or lightly flavored, optional

Instructions
 

  • Preheat your oven to 400°F. Line a baking sheet with parchment paper and lightly mist with nonstick spray.
  • Mix the wet ingredients: In a medium bowl, whisk together the Greek yogurt and eggs until smooth. Stir in the vanilla extract, if using.
  • Add the dry ingredients: Sprinkle the pancake mix evenly over the wet mixture. Add the cocoa powder, baking powder, and salt, then lightly mix those dry ingredients together on top (to help distribute the baking powder and cocoa evenly). Stir everything together until just combined.
  • Fold in the chocolate chips gently. The batter will be thick and dough-like—that’s exactly right.
  • Scoop the batter: Spray a ⅓-cup measuring scoop with nonstick spray, then drop equal mounds onto the prepared baking sheet, leaving a few inches of space between each. Shape slightly into rounded buns and press a few extra chocolate chips on top for that bakery-style finish.
  • Bake for about 15 minutes, or until the tops are just set.
  • Cool on the pan for about 10 minutes before removing.

Notes

*Muffin Option: You can also bake these in a standard 12-cup muffin tin. Divide the batter evenly among 8–10 compartments and bake for 15–18 minutes at 400°F.
• To Prevent Sticking
I recommend misting the parchment paper with nonstick oil spray to ensure the pastries don’t stick and are easy to remove once they’re done cooking and have slightly cooled on the counter.  I haven’t had any problems with sticking, but some people have written in to say they’ve had an issue so it’s worth misting the parchment paper to be extra cautious.
Yogurt Recommendations 
• Make sure your yogurt is very thick, and drain off any liquid from the top before mixing in with your eggs. I recommend vanilla Greek yogurt without any added sugar. Two brands I like using include Oikos Triple Zero and Chobani 20g.
• I’ve also tested this recipe using plain, unflavored, nonfat Greek yogurt. If you decide to give this a try, you’ll need to add 1 tsp of vanilla extract and 2 Tbsp of a sweetener. For the sweetener, I recommend maple syrup, but you could also use regular sugar, coconut sugar, or honey (although if you use honey, your breakfast pastries will have a honey-forward flavor, so be sure you love honey!). Since the vanilla and maple syrup will add extra liquid to your batter, add a few tablespoons of additional flour or pancake mix to thicken it back up. 
• Swaps for the Pancake Mix
I tested this recipe using lots of different substitutions for the protein pancake mix. Any of the following variations will work well—use the same one cup amount, unless otherwise specified. All of the straight flours (non-pancake mix varieties) will require an extra 1 teaspoon of baking powder, for a total of 3 teaspoons (or 1 Tablespoon).  
  • Standard pancake mix (not a protein type)
  • Standard gluten-free pancake mix (I used King Arthur, so I’m not sure if other brands will work as well)
  • All-purpose flour + 1 extra teaspoon baking powder (for a total of 3 tsp)
  • Bread flour+ 1 extra teaspoon baking powder (for a total of 3 tsp)
  • White-whole wheat flour+ 1 extra teaspoon baking powder (for a total of 3 tsp)
  • Whole wheat pastry flour + 1 extra teaspoon baking powder (for a total of 3 tsp)
  • Whole wheat flour + 1 extra teaspoon baking powder (for a total of 3 tsp)
  • Whole wheat flour (3/4 cup) + vanilla or chocolate-flavored protein powder (1/4 cup)+ 1 extra teaspoon baking powder (for a total of 3 tsp)
*Unfortunately, almond flour did not work for this recipe when I experimented with it; the batter became too thin and runny, and the resulting pastries were very flat.  
• Substitutes For Eggs
A few people have asked about a substitute for the eggs, and so I tested this recipe using both a “chia egg” and a “flax egg”. Either one will work!  There’s not really much of a difference in the texture or flavor of the final product—maybe I  detected a slightly chewier texture when using ground flaxseed over the chia seed.
Here’s how to make this substitute for the two eggs in this recipe: 
  • Combine 2 Tbsp of either chia seeds or ground flaxseed with 5 Tbsp water. (Both chia seeds and ground flax work for this recipe, but ground flax is preferred.)
  • Mix and let sit for at least 10 minutes to slightly firm into a gel.
Then, follow the rest of the recipe as normal. Just be sure to carefully beat the yogurt into the “chia/flax egg” until smooth. And when combining the wet and dry ingredients, the batter may appear a bit thick at first, but continue stirring and eventually it will all combine! 
• Regarding the shape: Don’t be surprised if your batch looks a little different each time—some days they rise higher and turn out puffier like buns, while other times they’re wider and flatter, more like jumbo cookies or thick pancakes. I’ve tried to crack the code, but there’s no clear reason behind it! The good news is that they taste equally delicious no matter how they bake up.
• Storage:
  • Fridge: Store in an airtight container for up to 5 days. Warm 10–15 seconds in the microwave for that warm, gooey chocolate experience.
  • Freezer: Freeze in a single layer, then transfer to a freezer bag or airtight container. Reheat in the microwave for about 30 seconds (or until warmed through) before serving.
• Variations:
  • Add a pinch of espresso powder for a mocha twist.
  • Stir in chopped walnuts or pecans for crunch.
  • Drizzle with melted dark chocolate after cooling for an extra-decadent finish.
Author: Joy Bauer, MS, RDN, CDN

Nutrition Information per serving

Serving Size: 1 pastryCalories: 160Carbohydrates: 23gProtein: 7gTotal Fat: 5g— Unsaturated Fat: 2.5g— Saturated Fat: 2.5gCholesterol: 45mgSodium: 250mgPotassium: 310mgFiber: 3gTotal Sugar: 10g— Natural Sugar: 4g— Added Sugar: 6gVitamin C: 3mgCalcium: 110mgIron: 1.5mg
Nutrition information is calculated using a leading industry software. That being said, brands can vary, and there may be slight fluctuations in the numbers.
I’m hoping you loved this recipe! If you made it and want to share feedback, I’d be so grateful to hear from you. Please leave a review below or tag @joybauer on Instagram!